Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 412 to 461 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
network_comparison
green
103 TRO trophinin. [swissprot;acc:q12816] Ranked 88.2482 1.24949 110.265
104 no value jun dimerization protein. [refseq;acc:nm_130469] Rooted 60.8365 1.27758 77.7233
HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 252.371 1.24926 202.016
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Measured 4241.57 1.36996 5810.79
PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Squared 407289 1.54656 263351
105 FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Rooted 60.8675 1.27682 77.7168
GNB1 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked 266.716 1.24914 333.165
MSI1 musashi 1. [refseq;acc:nm_002442] Measured 4241.57 1.36996 5810.79
PSCD2 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Squared 407289 1.54656 263351
106 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 252.329 1.24913 202.004
FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 1.27678 77.7165
PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Squared 407289 1.54656 263351
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 1.36996 5810.79
107 FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted 60.875 1.27664 77.7152
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 1.24907 201.998
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured 4266.04 1.36977 5843.51
PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared 407289 1.54656 263351
108 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 19321 1.54043 12542.6
CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted 49.2925 1.26585 62.397
FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Measured 4366.44 1.35116 5899.76
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 1.24902 201.995
109 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted 49.2923 1.26585 62.3969
GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Ranked 266.933 1.24856 333.281
MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 19321 1.54043 12542.6
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Measured 4366.44 1.35116 5899.76
110 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted 49.293 1.26585 62.3973
DTX2 deltex 2. [refseq;acc:nm_020892] Ranked 333.144 1.2459 267.393
MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 1.54043 12542.6
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured 4366.44 1.35116 5899.76
111 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted 49.2923 1.26585 62.3969
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked 332.925 1.24563 267.274
MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared 19321 1.54043 12542.6
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured 4366.44 1.35116 5899.76
112 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted 49.3267 1.26537 62.4167
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Squared 19321 1.54043 12542.6
PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Ranked 332.874 1.24557 267.246
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 1.35116 5899.76
113 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted 80.4705 1.26165 101.526
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 332.874 1.24557 267.246
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared 19321 1.54043 12542.6
114 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 80.4705 1.26165 101.526
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 332.874 1.24557 267.246
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 4300.47 1.35048 5807.72
115 KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked 332.874 1.24557 267.246
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 21185 1.34491 28492
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 1.54043 12542.6
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted 80.4705 1.26165 101.526
116 AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/